Voxel-based morphometry preprocessing for group comparison

Preparations

- Data needs to be in nifti (.nii) format before running anything in SPM.
- Save the script (.m file) that will save total grey matter volumes to your system

Open spm

% spm-8-4290

- it is useful to save each batch as you make it so that you can repeat on a different data set in the same way if necessary.


Step 1: Spatial normalisation

- Select 'Estimate and Write' on the spm buttons panel.
- Upload each subjects file into the 'Source Image' and 'Images to Write' options
- Select T1.nii as 'Template Image'
- Run
- These files save with a 'w' prefix

Step 2: Segmentation

- Under 'Output files' are grey matter, white matter and cerebrospinal fluid - for each select 'Native + Modulated and Unmodulated'
- Under clean up any partitions select 'Thorough Clean'
- This will save files with different prefixes (c1, c2, c3 - grey, white, CSF) and w - normalised, m-modulated -- use the 'wm' prefix for step 3.
- Before moving on to the smoothing step, you will need to write the GM volumes (for grey matter analysis) of each subject into a text file. To do this click the 'utils' tab and select all mwc1* files and then select 'save to txt file'. The files need to be selected in the same order as the design matrix to ensure the volumes correspond to the correct subject. (you may then want to edit the text file and delete everything except the volume measures).

Step 3: Smoothing

- Click the smoothing button, and select files with mwc1 (modulated, normalised grey matter) prefix.
- Keep default settings (i.e. 8mm FWHM)
- Press play button

Finally, you may also like to create a txt file with the vector for groups, e.g. 1 for patients, 0 for controls - ensure the same order as GM volume file and subject selection.